Dereplication. Question.

[SergeyBaikal]

I'm sorry, but I still don't get it. Is it necessary to do dereplication before launching the vRhyme? In my understanding, the pipelines look like this:

1. Spades

2. Virsorter2

3. Bowtie2

4. Dereplication contigs? (vRhyme script or CheckV scripts (ANI)) And is it possible to dereplicate using CheckV scripts?

5. vRhyme

6. vRhyme -i input_fasta -t threads -o output_folder/ --derep_only --method longest

7. vRhyme -i fasta -g genes -p proteins -b bam_folder/*.bam -t threads -o output_folder/

And separately complete genomes with DTR and ITR can be found in the file circular.tsv. I.e. we get a set of bins and a list of complete virus genomes as output?
I use metagenomes from the lake water.